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nextflow.config
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// Main driver script
manifest.mainScript = 'cpipes'
def fs = File.separator
def pd = "${projectDir}"
// Global parameters
includeConfig "${pd}${fs}conf${fs}manifest.config"
includeConfig "${pd}${fs}conf${fs}base.config"
// Include FASTQ config to prepare for a case when the entry point is
// FASTQ metadata CSV or FASTQ input directory
includeConfig "${pd}${fs}conf${fs}fastq.config"
if (params.pipeline != null) {
try {
includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
} catch (Exception e) {
System.err.println('-'.multiply(params.linewidth) + "\n" +
"\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
'-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
"default pipeline configuration. Please provide a pipeline \n" +
"name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth))
System.exit(1)
}
}
// Include modules' config last.
includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
includeConfig "${pd}${fs}conf${fs}modules.config"
// Nextflow runtime profiles
conda.cacheDir = "${pd}${fs}kondagac_cache"
singularity.cacheDir = "${pd}${fs}cingularitygac_cache"
profiles {
includeConfig "${pd}${fs}conf${fs}computeinfra.config"
}